In this talk, we will discuss the pros and cons of using whole genome sequencing (WGS) to predict the antimicrobial resistance (AMR) profile of bacterial pathogens, using methicillin-resistant Staphylococcus aureus (MRSA) causing bacteraemia as an example.
The Australian Staphylococcus aureus Surveillance Outcome Program (ASSOP) is one of the three active AMR national surveillance programs conducted by the Australian Group on Antimicrobial Resistance (AGAR). Participating laboratories across Australia collect S. aureus bacteraemia (SAB) isolates and patient metadata from each SAB episode. Antimicrobial susceptibility testing is performed on each SAB isolate using the Vitek® 2 or BD Phoenix™ automated systems. WGS is then performed to characterise the MRSA isolates.
In 2021, 48 institutions from all Australian states and mainland territories participated in ASSOP and a total of 2,928 SAB episodes were reported. Of the 495 MRSA, 472 isolates (95.4%) were available for WGS. WGS was performed using short-read sequencing technology on the NextSeq® 500 Illumina platform. The raw sequence reads were processed and analysed using various bioinformatics pipelines to identify the multi-locus sequence type (ST) of each isolate and the presence of genes and mutations associated with AMR and virulence. A comparison of the genotypic and phenotypic AMR profile of each MRSA isolate was then performed.